1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
use std::cmp;
use std::io;
use std::io::prelude::*;
use std::mem;

#[cfg(feature = "tokio")]
use futures::Poll;
#[cfg(feature = "tokio")]
use tokio_io::{AsyncRead, AsyncWrite};

use super::{GzBuilder, GzHeader};
use super::{FCOMMENT, FEXTRA, FHCRC, FNAME};
use crc::CrcReader;
use deflate;
use Compression;

fn copy(into: &mut [u8], from: &[u8], pos: &mut usize) -> usize {
    let min = cmp::min(into.len(), from.len() - *pos);
    for (slot, val) in into.iter_mut().zip(from[*pos..*pos + min].iter()) {
        *slot = *val;
    }
    *pos += min;
    return min;
}

pub(crate) fn corrupt() -> io::Error {
    io::Error::new(
        io::ErrorKind::InvalidInput,
        "corrupt gzip stream does not have a matching checksum",
    )
}

fn bad_header() -> io::Error {
    io::Error::new(io::ErrorKind::InvalidInput, "invalid gzip header")
}

fn read_le_u16<R: Read>(r: &mut R) -> io::Result<u16> {
    let mut b = [0; 2];
    r.read_exact(&mut b)?;
    Ok((b[0] as u16) | ((b[1] as u16) << 8))
}

pub(crate) fn read_gz_header<R: Read>(r: &mut R) -> io::Result<GzHeader> {
    let mut crc_reader = CrcReader::new(r);
    let mut header = [0; 10];
    crc_reader.read_exact(&mut header)?;

    let id1 = header[0];
    let id2 = header[1];
    if id1 != 0x1f || id2 != 0x8b {
        return Err(bad_header());
    }
    let cm = header[2];
    if cm != 8 {
        return Err(bad_header());
    }

    let flg = header[3];
    let mtime = ((header[4] as u32) << 0)
        | ((header[5] as u32) << 8)
        | ((header[6] as u32) << 16)
        | ((header[7] as u32) << 24);
    let _xfl = header[8];
    let os = header[9];

    let extra = if flg & FEXTRA != 0 {
        let xlen = read_le_u16(&mut crc_reader)?;
        let mut extra = vec![0; xlen as usize];
        crc_reader.read_exact(&mut extra)?;
        Some(extra)
    } else {
        None
    };
    let filename = if flg & FNAME != 0 {
        // wow this is slow
        let mut b = Vec::new();
        for byte in crc_reader.by_ref().bytes() {
            let byte = byte?;
            if byte == 0 {
                break;
            }
            b.push(byte);
        }
        Some(b)
    } else {
        None
    };
    let comment = if flg & FCOMMENT != 0 {
        // wow this is slow
        let mut b = Vec::new();
        for byte in crc_reader.by_ref().bytes() {
            let byte = byte?;
            if byte == 0 {
                break;
            }
            b.push(byte);
        }
        Some(b)
    } else {
        None
    };

    if flg & FHCRC != 0 {
        let calced_crc = crc_reader.crc().sum() as u16;
        let stored_crc = read_le_u16(&mut crc_reader)?;
        if calced_crc != stored_crc {
            return Err(corrupt());
        }
    }

    Ok(GzHeader {
        extra: extra,
        filename: filename,
        comment: comment,
        operating_system: os,
        mtime: mtime,
    })
}

/// A gzip streaming encoder
///
/// This structure exposes a [`BufRead`] interface that will read uncompressed data
/// from the underlying reader and expose the compressed version as a [`BufRead`]
/// interface.
///
/// [`BufRead`]: https://doc.rust-lang.org/std/io/trait.BufRead.html
///
/// # Examples
///
/// ```
/// use std::io::prelude::*;
/// use std::io;
/// use flate2::Compression;
/// use flate2::bufread::GzEncoder;
/// use std::fs::File;
/// use std::io::BufReader;
///
/// // Opens sample file, compresses the contents and returns a Vector or error
/// // File wrapped in a BufReader implements BufRead
///
/// fn open_hello_world() -> io::Result<Vec<u8>> {
///     let f = File::open("examples/hello_world.txt")?;
///     let b = BufReader::new(f);
///     let mut gz = GzEncoder::new(b, Compression::fast());
///     let mut buffer = Vec::new();
///     gz.read_to_end(&mut buffer)?;
///     Ok(buffer)
/// }
/// ```
#[derive(Debug)]
pub struct GzEncoder<R> {
    inner: deflate::bufread::DeflateEncoder<CrcReader<R>>,
    header: Vec<u8>,
    pos: usize,
    eof: bool,
}

pub fn gz_encoder<R: BufRead>(header: Vec<u8>, r: R, lvl: Compression) -> GzEncoder<R> {
    let crc = CrcReader::new(r);
    GzEncoder {
        inner: deflate::bufread::DeflateEncoder::new(crc, lvl),
        header: header,
        pos: 0,
        eof: false,
    }
}

impl<R: BufRead> GzEncoder<R> {
    /// Creates a new encoder which will use the given compression level.
    ///
    /// The encoder is not configured specially for the emitted header. For
    /// header configuration, see the `GzBuilder` type.
    ///
    /// The data read from the stream `r` will be compressed and available
    /// through the returned reader.
    pub fn new(r: R, level: Compression) -> GzEncoder<R> {
        GzBuilder::new().buf_read(r, level)
    }

    fn read_footer(&mut self, into: &mut [u8]) -> io::Result<usize> {
        if self.pos == 8 {
            return Ok(0);
        }
        let crc = self.inner.get_ref().crc();
        let ref arr = [
            (crc.sum() >> 0) as u8,
            (crc.sum() >> 8) as u8,
            (crc.sum() >> 16) as u8,
            (crc.sum() >> 24) as u8,
            (crc.amount() >> 0) as u8,
            (crc.amount() >> 8) as u8,
            (crc.amount() >> 16) as u8,
            (crc.amount() >> 24) as u8,
        ];
        Ok(copy(into, arr, &mut self.pos))
    }
}

impl<R> GzEncoder<R> {
    /// Acquires a reference to the underlying reader.
    pub fn get_ref(&self) -> &R {
        self.inner.get_ref().get_ref()
    }

    /// Acquires a mutable reference to the underlying reader.
    ///
    /// Note that mutation of the reader may result in surprising results if
    /// this encoder is continued to be used.
    pub fn get_mut(&mut self) -> &mut R {
        self.inner.get_mut().get_mut()
    }

    /// Returns the underlying stream, consuming this encoder
    pub fn into_inner(self) -> R {
        self.inner.into_inner().into_inner()
    }
}

#[inline]
fn finish(buf: &[u8; 8]) -> (u32, u32) {
    let crc = ((buf[0] as u32) << 0)
        | ((buf[1] as u32) << 8)
        | ((buf[2] as u32) << 16)
        | ((buf[3] as u32) << 24);
    let amt = ((buf[4] as u32) << 0)
        | ((buf[5] as u32) << 8)
        | ((buf[6] as u32) << 16)
        | ((buf[7] as u32) << 24);
    (crc, amt)
}

impl<R: BufRead> Read for GzEncoder<R> {
    fn read(&mut self, mut into: &mut [u8]) -> io::Result<usize> {
        let mut amt = 0;
        if self.eof {
            return self.read_footer(into);
        } else if self.pos < self.header.len() {
            amt += copy(into, &self.header, &mut self.pos);
            if amt == into.len() {
                return Ok(amt);
            }
            let tmp = into;
            into = &mut tmp[amt..];
        }
        match self.inner.read(into)? {
            0 => {
                self.eof = true;
                self.pos = 0;
                self.read_footer(into)
            }
            n => Ok(amt + n),
        }
    }
}

impl<R: BufRead + Write> Write for GzEncoder<R> {
    fn write(&mut self, buf: &[u8]) -> io::Result<usize> {
        self.get_mut().write(buf)
    }

    fn flush(&mut self) -> io::Result<()> {
        self.get_mut().flush()
    }
}

/// A gzip streaming decoder
///
/// This structure exposes a [`ReadBuf`] interface that will consume compressed
/// data from the underlying reader and emit uncompressed data.
///
/// [`ReadBuf`]: https://doc.rust-lang.org/std/io/trait.BufRead.html
///
/// # Examples
///
/// ```
/// use std::io::prelude::*;
/// use std::io;
/// # use flate2::Compression;
/// # use flate2::write::GzEncoder;
/// use flate2::bufread::GzDecoder;
///
/// # fn main() {
/// #   let mut e = GzEncoder::new(Vec::new(), Compression::default());
/// #   e.write_all(b"Hello World").unwrap();
/// #   let bytes = e.finish().unwrap();
/// #   println!("{}", decode_reader(bytes).unwrap());
/// # }
/// #
/// // Uncompresses a Gz Encoded vector of bytes and returns a string or error
/// // Here &[u8] implements BufRead
///
/// fn decode_reader(bytes: Vec<u8>) -> io::Result<String> {
///    let mut gz = GzDecoder::new(&bytes[..]);
///    let mut s = String::new();
///    gz.read_to_string(&mut s)?;
///    Ok(s)
/// }
/// ```
#[derive(Debug)]
pub struct GzDecoder<R> {
    inner: GzState,
    header: Option<GzHeader>,
    reader: CrcReader<deflate::bufread::DeflateDecoder<R>>,
    multi: bool
}

#[derive(Debug)]
enum GzState {
    Header(Vec<u8>),
    Body,
    Finished(usize, [u8; 8]),
    Err(io::Error),
    End
}

/// A small adapter which reads data originally from `buf` and then reads all
/// further data from `reader`. This will also buffer all data read from
/// `reader` into `buf` for reuse on a further call.
struct Buffer<'a, T: 'a> {
    buf: &'a mut Vec<u8>,
    buf_cur: usize,
    buf_max: usize,
    reader: &'a mut T
}

impl<'a, T> Buffer<'a, T> {
    fn new(buf: &'a mut Vec<u8>, reader: &'a mut T) -> Buffer<'a, T> {
        Buffer {
            reader,
            buf_cur: 0,
            buf_max: buf.len(),
            buf,
        }
    }
}

impl<'a, T: Read> Read for Buffer<'a, T> {
    fn read(&mut self, buf: &mut [u8]) -> io::Result<usize> {
        if self.buf_cur == self.buf_max {
            let len = self.reader.read(buf)?;
            self.buf.extend_from_slice(&buf[..len]);
            Ok(len)
        } else {
            let len = (&self.buf[self.buf_cur..self.buf_max]).read(buf)?;
            self.buf_cur += len;
            Ok(len)
        }
    }
}

impl<R: BufRead> GzDecoder<R> {
    /// Creates a new decoder from the given reader, immediately parsing the
    /// gzip header.
    pub fn new(mut r: R) -> GzDecoder<R> {
        let mut buf = Vec::with_capacity(10); // minimum header length
        let mut header = None;

        let result = {
            let mut reader = Buffer::new(&mut buf, &mut r);
            read_gz_header(&mut reader)
        };

        let state = match result {
            Ok(hdr) => {
                header = Some(hdr);
                GzState::Body
            },
            Err(ref err) if io::ErrorKind::WouldBlock == err.kind()
                => GzState::Header(buf),
            Err(err) => GzState::Err(err)
        };

        GzDecoder {
            inner: state,
            reader: CrcReader::new(deflate::bufread::DeflateDecoder::new(r)),
            multi: false,
            header
        }
    }

    fn multi(mut self, flag: bool) -> GzDecoder<R> {
        self.multi = flag;
        self
    }
}

impl<R> GzDecoder<R> {
    /// Returns the header associated with this stream, if it was valid
    pub fn header(&self) -> Option<&GzHeader> {
        self.header.as_ref()
    }

    /// Acquires a reference to the underlying reader.
    pub fn get_ref(&self) -> &R {
        self.reader.get_ref().get_ref()
    }

    /// Acquires a mutable reference to the underlying stream.
    ///
    /// Note that mutation of the stream may result in surprising results if
    /// this encoder is continued to be used.
    pub fn get_mut(&mut self) -> &mut R {
        self.reader.get_mut().get_mut()
    }

    /// Consumes this decoder, returning the underlying reader.
    pub fn into_inner(self) -> R {
        self.reader.into_inner().into_inner()
    }
}

impl<R: BufRead> Read for GzDecoder<R> {
    fn read(&mut self, into: &mut [u8]) -> io::Result<usize> {
        let GzDecoder { inner, header, reader, multi } = self;

        loop {
            *inner = match mem::replace(inner, GzState::End) {
                GzState::Header(mut buf) => {
                    let result = {
                        let mut reader = Buffer::new(&mut buf, reader.get_mut().get_mut());
                        read_gz_header(&mut reader)
                    };
                    let hdr = result
                        .map_err(|err| {
                            if io::ErrorKind::WouldBlock == err.kind() {
                                *inner = GzState::Header(buf);
                            }

                            err
                        })?;
                    *header = Some(hdr);
                    GzState::Body
                },
                GzState::Body => {
                    if into.is_empty() {
                        *inner = GzState::Body;
                        return Ok(0);
                    }

                    let n = reader.read(into)
                        .map_err(|err| {
                            if io::ErrorKind::WouldBlock == err.kind() {
                                *inner = GzState::Body;
                            }

                            err
                        })?;

                    match n {
                        0 => GzState::Finished(0, [0; 8]),
                        n => {
                            *inner = GzState::Body;
                            return Ok(n);
                        }
                    }
                },
                GzState::Finished(pos, mut buf) => if pos < buf.len() {
                    let n = reader.get_mut().get_mut()
                        .read(&mut buf[pos..])
                        .and_then(|n| if n == 0 {
                            Err(io::ErrorKind::UnexpectedEof.into())
                        } else {
                            Ok(n)
                        })
                        .map_err(|err| {
                            if io::ErrorKind::WouldBlock == err.kind() {
                                *inner = GzState::Finished(pos, buf);
                            }

                            err
                        })?;

                    GzState::Finished(pos + n, buf)
                } else {
                    let (crc, amt) = finish(&buf);

                    if crc != reader.crc().sum() || amt != reader.crc().amount() {
                        return Err(corrupt());
                    } else if *multi {
                        let is_eof = reader.get_mut().get_mut()
                            .fill_buf()
                            .map(|buf| buf.is_empty())
                            .map_err(|err| {
                                if io::ErrorKind::WouldBlock == err.kind() {
                                    *inner = GzState::Finished(pos, buf);
                                }

                                err
                            })?;

                        if is_eof {
                            GzState::End
                        } else {
                            reader.reset();
                            reader.get_mut().reset_data();
                            header.take();
                            GzState::Header(Vec::with_capacity(10))
                        }
                    } else {
                        GzState::End
                    }
                },
                GzState::Err(err) => return Err(err),
                GzState::End => return Ok(0)
            };
        }
    }
}

#[cfg(feature = "tokio")]
impl<R: AsyncRead + BufRead> AsyncRead for GzDecoder<R> {}

impl<R: BufRead + Write> Write for GzDecoder<R> {
    fn write(&mut self, buf: &[u8]) -> io::Result<usize> {
        self.get_mut().write(buf)
    }

    fn flush(&mut self) -> io::Result<()> {
        self.get_mut().flush()
    }
}

#[cfg(feature = "tokio")]
impl<R: AsyncWrite + BufRead> AsyncWrite for GzDecoder<R> {
    fn shutdown(&mut self) -> Poll<(), io::Error> {
        self.get_mut().shutdown()
    }
}

/// A gzip streaming decoder that decodes all members of a multistream
///
/// A gzip member consists of a header, compressed data and a trailer. The [gzip
/// specification](https://tools.ietf.org/html/rfc1952), however, allows multiple
/// gzip members to be joined in a single stream. `MultiGzDecoder` will
/// decode all consecutive members while `GzDecoder` will only decompress
/// the first gzip member. The multistream format is commonly used in
/// bioinformatics, for example when using the BGZF compressed data.
///
/// This structure exposes a [`BufRead`] interface that will consume all gzip members
/// from the underlying reader and emit uncompressed data.
///
/// [`BufRead`]: https://doc.rust-lang.org/std/io/trait.BufRead.html
///
/// # Examples
///
/// ```
/// use std::io::prelude::*;
/// use std::io;
/// # use flate2::Compression;
/// # use flate2::write::GzEncoder;
/// use flate2::bufread::MultiGzDecoder;
///
/// # fn main() {
/// #   let mut e = GzEncoder::new(Vec::new(), Compression::default());
/// #   e.write_all(b"Hello World").unwrap();
/// #   let bytes = e.finish().unwrap();
/// #   println!("{}", decode_reader(bytes).unwrap());
/// # }
/// #
/// // Uncompresses a Gz Encoded vector of bytes and returns a string or error
/// // Here &[u8] implements BufRead
///
/// fn decode_reader(bytes: Vec<u8>) -> io::Result<String> {
///    let mut gz = MultiGzDecoder::new(&bytes[..]);
///    let mut s = String::new();
///    gz.read_to_string(&mut s)?;
///    Ok(s)
/// }
/// ```
#[derive(Debug)]
pub struct MultiGzDecoder<R>(GzDecoder<R>);

impl<R: BufRead> MultiGzDecoder<R> {
    /// Creates a new decoder from the given reader, immediately parsing the
    /// (first) gzip header. If the gzip stream contains multiple members all will
    /// be decoded.
    pub fn new(r: R) -> MultiGzDecoder<R> {
        MultiGzDecoder(GzDecoder::new(r).multi(true))
    }
}

impl<R> MultiGzDecoder<R> {
    /// Returns the current header associated with this stream, if it's valid
    pub fn header(&self) -> Option<&GzHeader> {
        self.0.header()
    }

    /// Acquires a reference to the underlying reader.
    pub fn get_ref(&self) -> &R {
        self.0.get_ref()
    }

    /// Acquires a mutable reference to the underlying stream.
    ///
    /// Note that mutation of the stream may result in surprising results if
    /// this encoder is continued to be used.
    pub fn get_mut(&mut self) -> &mut R {
        self.0.get_mut()
    }

    /// Consumes this decoder, returning the underlying reader.
    pub fn into_inner(self) -> R {
        self.0.into_inner()
    }
}

impl<R: BufRead> Read for MultiGzDecoder<R> {
    fn read(&mut self, into: &mut [u8]) -> io::Result<usize> {
        self.0.read(into)
    }
}

#[cfg(feature = "tokio")]
impl<R: AsyncRead + BufRead> AsyncRead for MultiGzDecoder<R> {}

impl<R: BufRead + Write> Write for MultiGzDecoder<R> {
    fn write(&mut self, buf: &[u8]) -> io::Result<usize> {
        self.get_mut().write(buf)
    }

    fn flush(&mut self) -> io::Result<()> {
        self.get_mut().flush()
    }
}

#[cfg(feature = "tokio")]
impl<R: AsyncWrite + BufRead> AsyncWrite for MultiGzDecoder<R> {
    fn shutdown(&mut self) -> Poll<(), io::Error> {
        self.get_mut().shutdown()
    }
}